Something wrong with the cache hidden ranges?
I'm just going through and updating my PQ's according to http://geocaching.com.au/stats/range/
and I seem to be coming up short to the numbers you have. Take the third NSW 1000 cache query. The GCA list says it should return 995 caches and I have just run it and it is returning 833 caches.
Perhaps there are a heap of caches that should be archived on GCA? Or just a problem with the calc?